José Antonio Camacho aligned an unsual line-up with Vadocz and Punal in central midfield and Nekounam playing behind the lone striker Pandiani.
The league leaders completely dominated the first half but were unable to find a way through until Samuel Eto'o's crucial strike seconds before the half time whistle.
They should have taken the lead after 10 minutes when Lionel Messi made a superb run past two defenders and beat the keeper but his effort was denied by the goalpost.
Walter Pandiani was in good position to schock the visitors but his header was saved by Victor Valdés and that was Osasuna's only chance of the first half.
All the action was at the other end and the Catalans finally broke the deadlock in the 45 minutes when Lionel Messi deliverved the ball to Samuel Eto'o who unleashed a hard shot from the edge the box to beat Roberto.
Osasuna begun the second half strongly and looked much more confident.
Camacho's men levelled the score on the hour mark when Javier Flano perfectly headed home Portillo's corner.
Barca took a while to react and the hosts took the lead in the 73rd minute. Walter Pandiani redirected Juanfran's set up behind Victor Valdés to the joy of the 20 000 fans in the Reyno de Navarra stadium.
The celebrations were short, the best team in Spain quickly cancelled the hosts lead thanks to Xavi who found the back of the net from a close range.
Five minutes before time, Shojaei lost a challenge and the ball went to Lionel Messi who scored the winner with spectacular strike from outside the box.
Javad Nekounam played the full match. The Iranian midfielder started in an unsual position and was not very effective until he switched back to his usual position in the second half. From that moment Osasuna's midfield was more stable and the men from Pamplona scored two goals.
His compatriot Shojaei had a short appearance, the 24-year-old was introduced after 82 minutes to replace the injured Plasil and should be partly blamed for Barcelona's third goal.